Sodium in PDB 4c7a: Crystal Structure of the Smoothened Crd, Selenomethionine- Labeled

The structure of Crystal Structure of the Smoothened Crd, Selenomethionine- Labeled, PDB code: 4c7a was solved by S.Nachtergaele, D.M.Whalen, L.K.Mydock, Z.Zhao, T.Malinauskas, K.Krishnan, P.W.Ingham, D.F.Covey, R.Rohatgi, C.Siebold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.47 / 2.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.130, 68.130, 92.270, 90.00, 90.00, 90.00
R / Rfree (%)	23.586 / 28.406

The structure of Crystal Structure of the Smoothened Crd, Selenomethionine- Labeled also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Smoothened Crd, Selenomethionine- Labeled (pdb code 4c7a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Smoothened Crd, Selenomethionine- Labeled, PDB code: 4c7a:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Smoothened Crd, Selenomethionine- Labeled


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Smoothened Crd, Selenomethionine- Labeled within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1159 b:51.7 occ:1.00 O A:SER74 2.1 49.5 1.0 O A:ALA71 2.6 46.3 1.0 O A:LEU68 2.6 47.7 1.0 C A:SER74 3.3 52.5 1.0 C A:LEU68 3.4 46.1 1.0 C A:ALA71 3.7 46.2 1.0 CB A:LEU68 3.7 49.1 1.0 CA A:LEU68 4.2 47.0 1.0 N A:GLU75 4.2 54.4 1.0 CA A:GLU75 4.2 57.7 1.0 N A:ILE69 4.3 46.5 1.0 N A:SER74 4.3 50.1 1.0 CA A:SER74 4.3 51.1 1.0 CA A:GLU72 4.4 55.0 1.0 CA A:ILE69 4.4 50.9 1.0 N A:GLU72 4.4 51.2 1.0 CA A:ALA71 4.6 44.0 1.0 C A:ILE69 4.7 48.0 1.0 N A:ALA71 4.7 43.5 1.0 C A:GLU72 4.8 53.5 1.0 O A:ILE69 4.8 51.0 1.0 CB A:SER74 4.8 48.6 1.0 CG A:GLU75 4.8 70.4 1.0 CB A:ALA71 4.9 41.3 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Smoothened Crd, Selenomethionine- Labeled


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Smoothened Crd, Selenomethionine- Labeled within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1158 b:40.3 occ:1.00 O B:VAL107 2.5 30.9 1.0 O B:SER67 2.7 30.7 1.0 N B:LEU70 3.2 35.4 1.0 C B:LEU68 3.3 32.7 1.0 CB B:LEU70 3.4 35.4 1.0 N B:ALA71 3.4 34.2 1.0 CA B:LEU68 3.4 31.7 1.0 CD B:PRO110 3.6 33.0 1.0 O B:LEU68 3.6 37.0 1.0 CA B:LEU70 3.6 35.7 1.0 N B:ILE69 3.7 34.9 1.0 C B:SER67 3.7 30.4 1.0 C B:VAL107 3.7 34.3 1.0 CG B:PRO110 3.8 34.6 1.0 CG B:LEU70 3.9 36.2 1.0 C B:LEU70 3.9 35.8 1.0 N B:LEU68 4.0 30.1 1.0 O B:TYR108 4.0 31.4 1.0 CB B:ALA71 4.0 33.0 1.0 C B:ILE69 4.2 35.6 1.0 C B:TYR108 4.2 32.6 1.0 CA B:TYR108 4.3 33.6 1.0 CA B:ALA71 4.4 34.0 1.0 N B:TYR108 4.4 35.3 1.0 CD1 B:LEU70 4.5 35.8 1.0 CA B:ILE69 4.5 37.1 1.0 CD1 B:LEU68 4.7 30.3 1.0 CB B:LEU68 4.7 31.5 1.0 CA B:VAL107 4.8 35.6 1.0 N B:MSE109 4.9 32.9 1.0 O B:LEU70 5.0 37.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Smoothened Crd, Selenomethionine- Labeled


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Smoothened Crd, Selenomethionine- Labeled within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1159 b:37.1 occ:1.00 O B:ALA71 2.2 30.8 1.0 O B:SER74 2.2 30.2 1.0 O B:LEU68 2.3 37.0 1.0 O B:HOH2005 2.3 38.9 1.0 O B:HOH2004 2.5 34.7 1.0 C B:ALA71 3.3 33.3 1.0 C B:LEU68 3.3 32.7 1.0 C B:SER74 3.4 31.3 1.0 CB B:LEU68 3.8 31.5 1.0 N B:GLU72 4.1 36.2 1.0 CA B:GLU72 4.1 39.1 1.0 N B:ILE69 4.1 34.9 1.0 CA B:ILE69 4.1 37.1 1.0 CA B:LEU68 4.2 31.7 1.0 N B:SER74 4.2 31.5 1.0 N B:ALA71 4.2 34.2 1.0 CA B:SER74 4.2 30.6 1.0 CA B:ALA71 4.3 34.0 1.0 N B:GLU75 4.3 33.6 1.0 C B:ILE69 4.3 35.6 1.0 O B:ILE69 4.4 36.3 1.0 CA B:GLU75 4.4 34.1 1.0 C B:GLU72 4.6 38.8 1.0 CB B:ALA71 4.6 33.0 1.0 CB B:SER74 4.8 30.9 1.0 N B:LEU70 4.9 35.4 1.0 CG B:LEU68 5.0 30.8 1.0 N B:ASP73 5.0 36.9 1.0

S.Nachtergaele, D.M.Whalen, L.K.Mydock, Z.Zhao, T.Malinauskas, K.Krishnan, P.W.Ingham, D.F.Covey, C.Siebold, R.Rohatgi. Structure and Function of the Smoothened Extracellular Domain in Vertebrate Hedgehog Signaling Elife V. 2 01340 2013.
ISSN: ISSN 2050-084X
PubMed: 24171105
DOI: 10.7554/ELIFE.01340